Merge pull request #276 from mrc-ide/mrc-3729

Fix lint
mrc-ide · Oct 26, 2022 · 76a6a83 · 76a6a83
2 parents 35d1847 + 0881ac1
commit 76a6a83
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Showing 23 changed files with 207 additions and 142 deletions.
diff --git a/.lintr b/.lintr
@@ -1,8 +1,7 @@
-linters: with_defaults(
+linters: linters_with_defaults(
     object_name_linter = NULL,
     object_length_linter = NULL,
     object_usage_linter = NULL,
-    todo_comment_linter = NULL,
     cyclocomp_linter = NULL
     )
-exclusions: list("tests/testthat.R")
+exclusions: list("tests/testthat.R", "inst/template/odin_c.R")
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: odin
 Title: ODE Generation and Integration
-Version: 1.4.0
+Version: 1.4.1
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "rich.fitzjohn@gmail.com"),
              person("Thibaut", "Jombart", role = "ctb"),

diff --git a/R/dependencies.R b/R/dependencies.R
@@ -46,8 +46,9 @@ join_deps <- function(x) {
   stopifnot(is.list(x))
   x <- x[!vlapply(x, is.null)]
   ## This should never be triggered
-  ok <- vlapply(x, function(el)
-    identical(names(el), c("functions", "variables")))
+  ok <- vlapply(x, function(el) {
+    identical(names(el), c("functions", "variables"))
+  })
   stopifnot(all(ok))
   if (length(x) == 0L) {
     list(functions = character(0), variables = character(0))

diff --git a/R/generate_c_compiled.R b/R/generate_c_compiled.R
@@ -640,14 +640,16 @@ generate_c_compiled_metadata <- function(dat, rewrite) {
     ## TODO: we should generate out the the critical bits but that's
     ## another problem.  See the comments in
     ## support_check_interpolate_t
-    args_min <- c_fold_call("fmax", vcapply(dat$interpolate$min, function(x)
-      sprintf("%s[0]", rewrite(x))))
+    args_min <- c_fold_call("fmax", vcapply(dat$interpolate$min, function(x) {
+      sprintf("%s[0]", rewrite(x))
+    }))
     if (length(dat$interpolate$max) == 0) {
       args_max <- "R_PosInf"
     } else {
-      args_max <- c_fold_call("fmin", vcapply(dat$interpolate$max, function(x)
+      args_max <- c_fold_call("fmin", vcapply(dat$interpolate$max, function(x) {
         sprintf("%s[%s - 1]", rewrite(x),
-                rewrite(dat$data$elements[[x]]$dimnames$length))))
+                rewrite(dat$data$elements[[x]]$dimnames$length))
+      }))
     }
 
     body$add("SEXP interpolate_t = PROTECT(allocVector(VECSXP, 3));")
@@ -700,8 +702,9 @@ generate_c_compiled_library <- function(dat, is_package) {
   }
   if (dat$features$has_user && dat$features$has_array) {
     d <- dat$data$elements
-    user_arrays <- any(vlapply(dat$equations, function(x)
-      !is.null(x$user) && d[[x$name]]$rank > 0))
+    user_arrays <- any(vlapply(dat$equations, function(x) {
+      !is.null(x$user) && d[[x$name]]$rank > 0
+    }))
     if (user_arrays) {
       v <- c(v, "user_get_array_dim",
              "user_get_array", "user_get_array_check",
@@ -715,8 +718,8 @@ generate_c_compiled_library <- function(dat, is_package) {
     v <- c(v, "interpolate_check_y")
   }
 
-  used <- unique(unlist(lapply(dat$equations, function(x)
-    x$depends$functions), FALSE, FALSE))
+  used <- unique(unlist(lapply(dat$equations, function(x) x$depends$functions),
+                        FALSE, FALSE))
   if ("%%" %in% used) {
     v <- c(v, "fmodr")
   }
@@ -746,8 +749,9 @@ generate_c_compiled_library <- function(dat, is_package) {
       nms <- vcapply(extra, "[[", "name")
       extra_lib <- list(
         declarations = set_names(vcapply(extra, "[[", "declaration"), nms),
-        definitions = set_names(vcapply(extra, function(x)
-          paste0(x$definition, "\n", collapse = "")), nms))
+        definitions = set_names(vcapply(extra, function(x) {
+          paste0(x$definition, "\n", collapse = "")
+        }), nms))
       lib <- join_library(list(lib, extra_lib))
     }
   }

diff --git a/R/generate_c_equation.R b/R/generate_c_equation.R
@@ -80,8 +80,9 @@ generate_c_equation_inplace_rmhyper <- function(eq, lhs, data_info, dat,
 
 generate_c_equation_array <- function(eq, data_info, dat, rewrite) {
   lhs <- generate_c_equation_array_lhs(eq, data_info, dat, rewrite)
-  lapply(eq$rhs, function(x)
-    generate_c_equation_array_rhs(x$value, x$index, lhs, rewrite))
+  lapply(eq$rhs, function(x) {
+    generate_c_equation_array_rhs(x$value, x$index, lhs, rewrite)
+  })
 }
 
 
@@ -447,7 +448,7 @@ generate_c_equation_delay_discrete <- function(eq, data_info, dat, rewrite) {
     advance,
     sprintf_safe("double * %s;", tail),
     c_expr_if(time_check, data_initial, data_offset),
-    assign) -> ret
+    assign)
 }
 
 

diff --git a/R/generate_c_support.R b/R/generate_c_support.R
@@ -12,8 +12,9 @@ generate_c_support_sum <- function(rank) {
   ## here, though in general they are not needed as function scope
   ## avoids the worst of things.
   index <- INDEX[i]
-  mult <- vcapply(seq_len(rank), function(x)
-    array_dim_name("x", paste(seq_len(x - 1), collapse = "")))
+  mult <- vcapply(seq_len(rank), function(x) {
+    array_dim_name("x", paste(seq_len(x - 1), collapse = ""))
+  })
   counter <- vcapply(index, strrep, n = 2, USE.NAMES = FALSE)
 
   limits <- rbind(sprintf_safe("from_%s", index),

diff --git a/R/generate_js.R b/R/generate_js.R
@@ -17,10 +17,11 @@ generate_js <- function(ir, options) {
   eqs <- generate_js_equations(dat, rewrite)
   core <- generate_js_core(eqs, dat, rewrite)
 
-  internal_dim_elements <- vlapply(dat$data$elements, function(x)
+  internal_dim_elements <- vlapply(dat$data$elements, function(x) {
     x$location == "internal" &&
     x$storage_type %in% c("double", "int", "bool") &&
-    x$rank > 1)
+    x$rank > 1
+  })
   internal_dim <- lapply(dat$data$elements[internal_dim_elements],
                          function(x) x$dimnames$dim)
 
@@ -203,26 +204,28 @@ generate_js_core_update_metadata <- function(eqs, dat, rewrite) {
   }
 
   if (dat$features$has_interpolate) {
-    args_min <- js_fold_call("Math.max",
-                             vcapply(dat$interpolate$min, function(x)
-                               sprintf("%s[0]", rewrite(x))))
+    args_min <- js_fold_call(
+      "Math.max",
+      vcapply(dat$interpolate$min, function(x) sprintf("%s[0]", rewrite(x))))
     if (length(dat$interpolate$max) == 0) {
       args_max <- "Infinity"
     } else {
       args_max <- js_fold_call(
         "Math.min",
-        vcapply(dat$interpolate$max, function(x)
+        vcapply(dat$interpolate$max, function(x) {
           sprintf("%s[%s - 1]", rewrite(x),
-                  rewrite(dat$data$elements[[x]]$dimnames$length))))
+                  rewrite(dat$data$elements[[x]]$dimnames$length))
+        }))
     }
   }
 
   len_block <- function(location) {
     if (location == "internal") {
       ## This excludes interpolate_data and ring_buffer
-      keep <- vlapply(dat$data$elements, function(x)
+      keep <- vlapply(dat$data$elements, function(x) {
         x$location == "internal" &&
-        x$storage_type %in% c("double", "int", "bool"))
+          x$storage_type %in% c("double", "int", "bool")
+      })
       contents <- dat$data$elements[keep]
     } else {
       contents <- dat$data$elements[names(dat$data[[location]]$contents)]
@@ -240,11 +243,13 @@ generate_js_core_update_metadata <- function(eqs, dat, rewrite) {
   body$add(len_block("output"))
 
   if (dat$features$has_interpolate) {
-    args_min <- vcapply(dat$interpolate$min, function(x)
-      sprintf("%s[0]", rewrite(x)))
-    args_max <- vcapply(dat$interpolate$max, function(x)
+    args_min <- vcapply(dat$interpolate$min, function(x) {
+      sprintf("%s[0]", rewrite(x))
+    })
+    args_max <- vcapply(dat$interpolate$max, function(x) {
       sprintf("%s[%s - 1]", rewrite(x),
-              rewrite(dat$data$elements[[x]]$dimnames$length)))
+              rewrite(dat$data$elements[[x]]$dimnames$length))
+    })
     array <- function(x) {
       sprintf("[%s]", paste(x, collapse = ", "))
     }

diff --git a/R/generate_js_equation.R b/R/generate_js_equation.R
@@ -116,8 +116,9 @@ generate_js_equation_user <- function(eq, data_info, dat, rewrite) {
 
 generate_js_equation_array <- function(eq, data_info, dat, rewrite) {
   lhs <- generate_js_equation_array_lhs(eq, data_info, dat, rewrite)
-  lapply(eq$rhs, function(x)
-    generate_js_equation_array_rhs(x$value, x$index, lhs, rewrite))
+  lapply(eq$rhs, function(x) {
+    generate_js_equation_array_rhs(x$value, x$index, lhs, rewrite)
+  })
 }
 
 

diff --git a/R/generate_r.R b/R/generate_r.R
@@ -267,16 +267,18 @@ generate_r_interpolate_t <- function(dat, env, rewrite) {
     return(function(...) NULL)
   }
 
-  args_min <- lapply(dat$interpolate$min, function(x)
-    call("[[", rewrite(x), 1L))
+  args_min <- lapply(dat$interpolate$min, function(x) {
+    call("[[", rewrite(x), 1L)
+  })
   if (length(args_min) == 1L) {
     min <- args_min[[1L]]
   } else {
     min <- as.call(c(list(quote(max)), args_min))
   }
 
-  args_max <- lapply(dat$interpolate$max, function(x)
-    call("[[", rewrite(x), call("length", rewrite(x))))
+  args_max <- lapply(dat$interpolate$max, function(x) {
+    call("[[", rewrite(x), call("length", rewrite(x)))
+  })
   if (length(args_max) == 0L) {
     max <- Inf
   } else if (length(args_max) == 1L) {
@@ -310,10 +312,11 @@ generate_r_set_initial <- function(dat, env, rewrite) {
 
   set_y <- call(
     "if", call("!", call("is.null", as.name(dat$meta$state))),
-    r_expr_block(lapply(dat$data$variable$contents, function(x)
+    r_expr_block(lapply(dat$data$variable$contents, function(x) {
       call("<-", rewrite(x$initial),
            r_extract_variable(x, dat$data$elements, as.name(dat$meta$state),
-                              rewrite)))))
+                              rewrite))
+    })))
   set_t <- call("<-", rewrite(dat$meta$initial_time), as.name(dat$meta$time))
 
   body <- list(set_y, set_t)

diff --git a/R/generate_r_equation.R b/R/generate_r_equation.R
@@ -53,8 +53,9 @@ generate_r_equation_inplace <- function(eq, data_info, dat, rewrite) {
 
 generate_r_equation_array <- function(eq, data_info, dat, rewrite) {
   lhs <- generate_r_equation_array_lhs(eq, data_info, dat, rewrite)
-  lapply(eq$rhs, function(x)
-    generate_r_equation_array_rhs(x$value, x$index, lhs, rewrite))
+  lapply(eq$rhs, function(x) {
+    generate_r_equation_array_rhs(x$value, x$index, lhs, rewrite)
+  })
 }
 
 
@@ -143,7 +144,7 @@ generate_r_equation_copy <- function(eq, data_info, dat, rewrite) {
 
   if (data_info$rank == 0) {
     lhs <- call("[[", storage, r_offset_to_position(offset))
-  } else{
+  } else {
     i <- call("seq_len", rewrite(data_info$dimnames$length))
     lhs <- call("[", storage, call("+", offset, i))
   }